org.forester.msa

Class Mafft

java.lang.Object

org.forester.msa.MsaInferrer

org.forester.msa.Mafft

public final class Mafft
extends MsaInferrer

Method Summary

Modifier and Type	Method and Description
static MsaInferrer	createInstance(String path_to_prg)
static String	getDefaultParameters()
String	getErrorDescription()
int	getExitCode()
Msa	infer(File path_to_input_seqs, List<String> opts)
Msa	infer(List<MolecularSequence> seqs, List<String> opts)

Methods inherited from class org.forester.msa.MsaInferrer

clone, isInstalled

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

createInstance

public static MsaInferrer createInstance(String path_to_prg)
                                  throws IOException

Throws:

IOException

getDefaultParameters

public static String getDefaultParameters()

getErrorDescription

public String getErrorDescription()

Specified by:

getErrorDescription in class MsaInferrer

getExitCode

public int getExitCode()

Specified by:

getExitCode in class MsaInferrer

infer

public Msa infer(List<MolecularSequence> seqs,
                 List<String> opts)
          throws IOException,
                 InterruptedException

Specified by:

infer in class MsaInferrer

Throws:

IOException

InterruptedException

infer

public Msa infer(File path_to_input_seqs,
                 List<String> opts)
          throws IOException,
                 InterruptedException

Specified by:

infer in class MsaInferrer

Throws:

IOException

InterruptedException